I installed bowtie2 and when running tophat I get the following error:

Error in tophat:

[2012-06-19 14:02:39] Beginning TopHat run (v2.0.3)
[2012-06-19 14:02:39] Checking for Bowtie
                  Bowtie version:
[2012-06-19 14:02:39] Checking for Samtools
                Samtools version:
[2012-06-19 14:02:39] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files

I was wondering if I can create the index files using bowtie2 via command
line and then change the universe_wsgi.ini to:
 # Temporary files are stored in this directory.
    new_file_path = database/tmp

and put the index files there. Anyway, why is it not creating the indexes?
I created links to all bowtie2 executable files. If I remove bowtie 0.12.8,
then I get a error from tophat (bowtie not installed). Is it creating the
index with bowtie 0.12.8?
Thank you.

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